Contacts of the helix formed by residues 137 - 145 (chain F) in PDB entry 3LUE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 137 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ASP* 4.3 5.7 - - - +
12F ASN 4.0 17.5 + - - -
13F GLY* 5.9 1.4 - - - -
74F GLY* 5.1 3.8 + - - -
106F THR* 3.8 13.3 + - - +
107F GLU* 3.0 34.9 + - - +
108F ALA* 3.3 10.7 - - - +
109F PRO* 4.8 1.7 - - + +
135F ALA 4.5 0.2 - - - -
136F ILE* 1.3 72.7 - - - +
138F ALA* 1.4 61.5 + - - +
140F LEU* 3.2 14.6 + - - +
141F SER 3.3 8.8 + - - -
154F ASP* 2.9 10.6 - - - +
156F GLY* 4.0 21.5 - - - -
157F ASP 5.0 2.2 + - - +
339F VAL* 3.4 38.6 - - + +
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Residues in contact with ALA 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F PRO* 4.8 0.4 - - + -
136F ILE* 3.5 8.8 - - + +
137F GLN* 1.4 70.3 - - - +
139F VAL* 1.3 61.6 + - - +
141F SER* 3.3 5.0 + - - -
142F LEU* 3.1 18.2 + - - +
152F VAL* 3.5 15.8 - - + +
154F ASP* 1.5 66.5 + - + +
161F HIS* 4.7 3.4 - - + +
163F VAL* 5.0 7.6 - - + -
300F SER* 3.6 1.6 - - - +
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Residues in contact with VAL 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D VAL 4.9 6.7 - - - +
45D VAL* 3.1 18.9 - - - +
135F ALA* 6.1 1.3 - - + -
136F ILE* 3.5 25.2 + - + +
137F GLN 3.3 1.0 - - - -
138F ALA* 1.3 77.5 - - - +
140F LEU* 1.3 58.3 + - + +
142F LEU* 3.6 4.6 - - - +
143F TYR* 3.3 10.5 + - + +
163F VAL* 3.6 38.6 - - + -
165F ILE* 5.3 1.6 - - + -
170F ALA* 4.8 7.2 - - + -
375F PHE* 4.7 21.1 - - + -
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Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 5.2 0.4 - - + -
104F LEU* 3.9 6.5 - - + -
106F THR* 3.3 30.7 - - + -
135F ALA* 3.4 21.5 - - + -
136F ILE 2.9 30.1 - - - +
137F GLN 3.2 5.1 + - - +
139F VAL* 1.3 77.0 - - + +
141F SER* 1.3 66.0 + - - +
142F LEU 3.3 0.4 - - - -
143F TYR* 4.5 3.8 - - - +
144F ALA* 3.1 19.6 + - - +
338F SER 4.2 1.1 - - - -
339F VAL* 3.3 24.9 - - + +
342F GLY* 3.1 15.1 - - - +
343F GLY* 3.6 27.4 - - - +
346F LEU* 5.7 5.2 - - + -
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Residues in contact with SER 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D VAL* 2.4 21.5 - - - +
137F GLN 3.3 2.2 + - - -
138F ALA 3.3 5.8 + - - -
140F LEU* 1.3 78.3 - - - +
142F LEU* 1.3 54.1 + - - -
144F ALA* 3.5 3.3 + - - +
145F SER* 3.4 15.2 + - - -
154F ASP* 3.4 1.0 + - - -
300F SER* 2.8 42.3 + - - -
338F SER* 3.6 23.0 + - - -
339F VAL* 3.2 24.3 - - - +
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL 3.1 1.8 - - - +
44D MET* 2.1 21.1 - - - -
45D VAL* 0.9 384.8 - - + +
47D MET 3.2 6.9 - - - +
138F ALA 3.1 4.3 + - - +
139F VAL 3.6 5.2 - - - +
141F SER* 1.3 67.5 - - - +
143F TYR* 1.3 63.6 + - - -
145F SER* 2.8 13.7 + - - -
152F VAL* 2.1 28.0 - - + -
165F ILE* 1.5 54.5 - - + -
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Residues in contact with TYR 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D GLN* 5.4 2.0 - - + -
42D GLY 3.4 15.7 - - - -
43D VAL* 3.6 21.9 + - + +
45D VAL* 1.9 13.3 - - - +
47D MET 3.6 8.0 - - - +
48D GLY* 4.3 1.4 - - - -
49D GLN* 0.5 204.4 + - + +
139F VAL* 3.3 13.5 + - + +
140F LEU* 4.1 7.4 - - - +
141F SER 3.6 0.2 - - - -
142F LEU 1.3 67.6 - - - +
144F ALA* 1.3 61.5 + - - +
145F SER 3.2 2.8 + - - -
168F GLY 4.7 0.4 - - - -
342F GLY 4.6 7.6 - - - +
345F ILE* 4.0 30.4 - - + +
346F LEU* 4.7 19.1 - - + -
349F LEU* 4.4 3.8 - - + -
101O PHE* 4.9 1.8 - - + +
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Residues in contact with ALA 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140F LEU 3.1 19.1 + - - +
141F SER* 3.8 5.8 - - - +
142F LEU 3.2 0.2 - - - -
143F TYR* 1.3 75.9 - - - +
145F SER* 1.3 56.9 + - - +
338F SER* 4.1 10.1 - - - +
341F ILE* 4.0 9.6 - - + -
342F GLY* 3.4 23.0 - - - +
345F ILE* 4.0 17.0 - - + +
100O ARG* 5.8 3.1 - - - +
101O PHE* 4.9 4.7 - - - -
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Residues in contact with SER 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D VAL* 2.7 12.1 - - - -
46D GLY* 2.7 34.9 + - - -
47D MET 3.5 12.6 - - - -
48D GLY* 4.2 3.6 - - - -
141F SER 3.4 8.4 + - - -
142F LEU 2.8 7.9 + - - -
143F TYR 4.0 1.6 - - - -
144F ALA* 1.3 79.8 - - - +
146F GLY* 1.3 60.9 + - - +
147F ARG* 1.9 15.8 + - - -
298F VAL* 5.7 4.3 - - - -
100O ARG* 4.8 2.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il